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Brennan K, Zheng H, Fahrner JA, Shin JH, Gentles AJ, Schaefer B, Sunwoo JB, Bernstein JA, Gevaert O. NSD1 mutations deregulate transcription and DNA methylation of bivalent developmental genes in Sotos syndrome. Hum Mol Genet 2022; 31:2164-2184. [PMID: 35094088 PMCID: PMC9262396 DOI: 10.1093/hmg/ddac026] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 01/04/2022] [Accepted: 01/19/2022] [Indexed: 11/13/2022] Open
Abstract
Sotos syndrome (SS), the most common overgrowth with intellectual disability (OGID) disorder, is caused by inactivating germline mutations of NSD1, which encodes a histone H3 lysine 36 methyltransferase. To understand how NSD1 inactivation deregulates transcription and DNA methylation (DNAm), and to explore how these abnormalities affect human development, we profiled transcription and DNAm in SS patients and healthy control individuals. We identified a transcriptional signature that distinguishes individuals with SS from controls and was also deregulated in NSD1-mutated cancers. Most abnormally expressed genes displayed reduced expression in SS; these downregulated genes consisted mostly of bivalent genes and were enriched for regulators of development and neural synapse function. DNA hypomethylation was strongly enriched within promoters of transcriptionally deregulated genes: overexpressed genes displayed hypomethylation at their transcription start sites while underexpressed genes featured hypomethylation at polycomb binding sites within their promoter CpG island shores. SS patients featured accelerated molecular aging at the levels of both transcription and DNAm. Overall, these findings indicate that NSD1-deposited H3K36 methylation regulates transcription by directing promoter DNA methylation, partially by repressing polycomb repressive complex 2 (PRC2) activity. These findings could explain the phenotypic similarity of SS to OGID disorders that are caused by mutations in PRC2 complex-encoding genes.
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Affiliation(s)
- Kevin Brennan
- Stanford Center for Biomedical Informatics Research, Department of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Hong Zheng
- Stanford Center for Biomedical Informatics Research, Department of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Jill A Fahrner
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - June Ho Shin
- Department of Otolaryngology – Head and Neck Surgery, Stanford University School of Medicine, Palo Alto, CA 94305, USA
| | - Andrew J Gentles
- Stanford Center for Biomedical Informatics Research, Department of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Bradley Schaefer
- Department of Pediatrics, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - John B Sunwoo
- Department of Otolaryngology – Head and Neck Surgery, Stanford University School of Medicine, Palo Alto, CA 94305, USA
| | - Jonathan A Bernstein
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Olivier Gevaert
- Stanford Center for Biomedical Informatics Research, Department of Medicine, Stanford University, Stanford, CA 94305, USA
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2
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Ondičová M, Irwin RE, Thursby SJ, Hilman L, Caffrey A, Cassidy T, McLaughlin M, Lees-Murdock DJ, Ward M, Murphy M, Lamers Y, Pentieva K, McNulty H, Walsh CP. Folic acid intervention during pregnancy alters DNA methylation, affecting neural target genes through two distinct mechanisms. Clin Epigenetics 2022; 14:63. [PMID: 35578268 PMCID: PMC9112484 DOI: 10.1186/s13148-022-01282-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 04/29/2022] [Indexed: 12/22/2022] Open
Abstract
Background We previously showed that continued folic acid (FA) supplementation beyond the first trimester of pregnancy appears to have beneficial effects on neurocognitive performance in children followed for up to 11 years, but the biological mechanism for this effect has remained unclear. Using samples from our randomized controlled trial of folic acid supplementation in second and third trimester (FASSTT), where significant improvements in cognitive and psychosocial performance were demonstrated in children from mothers supplemented in pregnancy with 400 µg/day FA compared with placebo, we examined methylation patterns from cord blood (CB) using the EPIC array which covers approximately 850,000 cytosine–guanine (CG) sites across the genome. Genes showing significant differences were verified using pyrosequencing and mechanistic approaches used in vitro to determine effects on transcription. Results FA supplementation resulted in significant differences in methylation, particularly at brain-related genes. Further analysis showed these genes split into two groups. In one group, which included the CES1 gene, methylation changes at the promoters were important for regulating transcription. We also identified a second group which had a characteristic bimodal profile, with low promoter and high gene body (GB) methylation. In the latter, loss of methylation in the GB is linked to decreases in transcription: this group included the PRKAR1B/HEATR2 genes and the dopamine receptor regulator PDE4C. Overall, methylation in CB also showed good correlation with methylation profiles seen in a published data set of late gestation foetal brain samples. Conclusion We show here clear alterations in DNA methylation at specific classes of neurodevelopmental genes in the same cohort of children, born to FA-supplemented mothers, who previously showed improved cognitive and psychosocial performance. Our results show measurable differences at neural genes which are important for transcriptional regulation and add to the supporting evidence for continued FA supplementation throughout later gestation. This trial was registered on 15 May 2013 at www.isrctn.com as ISRCTN19917787. Supplementary Information The online version contains supplementary material available at 10.1186/s13148-022-01282-y.
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Affiliation(s)
- Miroslava Ondičová
- Genomic Medicine Research Group, Ulster University, Coleraine, Northern Ireland, UK
| | - Rachelle E Irwin
- Genomic Medicine Research Group, Ulster University, Coleraine, Northern Ireland, UK
| | - Sara-Jayne Thursby
- Genomic Medicine Research Group, Ulster University, Coleraine, Northern Ireland, UK.,The Johns Hopkins University School of Medicine, Baltimore, USA
| | - Luke Hilman
- Genomic Medicine Research Group, Ulster University, Coleraine, Northern Ireland, UK
| | - Aoife Caffrey
- Nutrition Innovation Centre for Food and Health (NICHE), School of Biomedical Sciences, Ulster University, Coleraine, Northern Ireland, UK
| | - Tony Cassidy
- Psychology Institute, Ulster University, Coleraine, Northern Ireland, UK
| | - Marian McLaughlin
- Psychology Institute, Ulster University, Coleraine, Northern Ireland, UK
| | - Diane J Lees-Murdock
- Genomic Medicine Research Group, Ulster University, Coleraine, Northern Ireland, UK
| | - Mary Ward
- Nutrition Innovation Centre for Food and Health (NICHE), School of Biomedical Sciences, Ulster University, Coleraine, Northern Ireland, UK
| | - Michelle Murphy
- Unitat de Medicina Preventiva i Salut Pública, Facultat de Medicina i Ciències de La Salut, Universitat Rovira i Virgili, Reus, Spain
| | - Yvonne Lamers
- Food, Nutrition, and Health Program, Faculty of Land and Food Systems, The University of British Columbia, and British Columbia Children's Hospital Research Institute, Vancouver, BC, Canada
| | - Kristina Pentieva
- Nutrition Innovation Centre for Food and Health (NICHE), School of Biomedical Sciences, Ulster University, Coleraine, Northern Ireland, UK
| | - Helene McNulty
- Nutrition Innovation Centre for Food and Health (NICHE), School of Biomedical Sciences, Ulster University, Coleraine, Northern Ireland, UK
| | - Colum P Walsh
- Genomic Medicine Research Group, Ulster University, Coleraine, Northern Ireland, UK. .,Centre for Research and Development, Region Gävleborg/Uppsala University, Gävle, Sweden.
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3
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Transcriptional overlap links DNA hypomethylation with DNA hypermethylation at adjacent promoters in cancer. Sci Rep 2021; 11:17346. [PMID: 34462486 PMCID: PMC8405634 DOI: 10.1038/s41598-021-96844-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Accepted: 08/17/2021] [Indexed: 12/15/2022] Open
Abstract
Tumor development involves alterations in DNA methylation patterns, which include both gains (hypermethylation) and losses (hypomethylation) in different genomic regions. The mechanisms underlying these two opposite, yet co-existing, alterations in tumors remain unclear. While studying the human MAGEA6/GABRA3 gene locus, we observed that DNA hypomethylation in tumor cells can lead to the activation of a long transcript (CT-GABRA3) that overlaps downstream promoters (GABRQ and GABRA3) and triggers their hypermethylation. Overlapped promoters displayed increases in H3K36me3, a histone mark deposited during transcriptional elongation and known to stimulate de novo DNA methylation. Consistent with such a processive mechanism, increases in H3K36me3 and DNA methylation were observed over the entire region covered by the CT-GABRA3 overlapping transcript. Importantly, experimental induction of CT-GABRA3 by depletion of DNMT1 DNA methyltransferase, resulted in a similar pattern of regional DNA hypermethylation. Bioinformatics analyses in lung cancer datasets identified other genomic loci displaying this process of coupled DNA hypo/hypermethylation, and some of these included tumor suppressor genes, e.g. RERG and PTPRO. Together, our work reveals that focal DNA hypomethylation in tumors can indirectly contribute to hypermethylation of nearby promoters through activation of overlapping transcription, and establishes therefore an unsuspected connection between these two opposite epigenetic alterations.
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4
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Fang X, Poulsen R, Zhao L, Wang J, Rivkees SA, Wendler CC. Knockdown of DNA methyltransferase 1 reduces DNA methylation and alters expression patterns of cardiac genes in embryonic cardiomyocytes. FEBS Open Bio 2021. [PMID: 34235895 PMCID: PMC8329956 DOI: 10.1002/2211-5463.13252] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 06/14/2021] [Accepted: 07/07/2021] [Indexed: 12/12/2022] Open
Abstract
We previously found that DNA methyltransferase 3a (DNMT3a) plays an important role in regulating embryonic cardiomyocyte gene expression, morphology, and function. In this study, we investigated the role of the most abundant DNMT in mammalian cells, DNMT1, in these processes. It is known that DNMT1 is essential for embryonic development, during which it is involved in regulating cardiomyocyte DNA methylation and gene expression. We used siRNA to knock down DNMT1 expression in primary cultures of mouse embryonic cardiomyocytes. Immunofluorescence staining and multielectrode array were, respectively, utilized to evaluate cardiomyocyte growth and electrophysiology. RNA sequencing (RNA‐Seq) and multiplex bisulfite sequencing were, respectively, performed to examine gene expression and promoter methylation. At 72 h post‐transfection, reduction of DNMT1 expression decreased the number and increased the size of embryonic cardiomyocytes. Beat frequency and the amplitude of field action potentials were decreased by DNMT1 siRNA. RNA‐Seq analysis identified 801 up‐regulated genes and 494 down‐regulated genes in the DNMT1 knockdown cells when compared to controls. Pathway analysis of the differentially expressed genes revealed pathways that were associated with cell death and survival, cell morphology, cardiac function, and cardiac disease. Alternative splicing analysis identified 929 differentially expressed exons, including 583 up‐regulated exons and 308 down‐regulated exons. Moreover, decreased methylation levels were found in the promoters of cardiac genes Myh6, Myh7, Myh7b, Tnnc1, Tnni3, Tnnt2, Nppa, Nppb, mef2c, mef2d, Camta2, Cdkn1A, and Cdkn1C. Of these 13 genes, 6 (Myh6, Tnnc1, Tnni3, Tnnt2, Nppa, Nppb) and 1 (Cdkn1C) had increased or decreased gene expression, respectively. Altogether, these data show that DNMT1 is important in embryonic cardiomyocytes by regulating DNA methylation, gene expression, gene splicing, and cell function.
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Affiliation(s)
- Xiefan Fang
- Department of Pediatrics, Child Health Research Institute, College of Medicine, University of Florida, Gainesville, FL, USA.,Charles River Laboratories, Inc., Reno, NV, USA
| | - Ryan Poulsen
- Department of Pediatrics, Child Health Research Institute, College of Medicine, University of Florida, Gainesville, FL, USA
| | - Lu Zhao
- Charles River Laboratories, Inc., Reno, NV, USA
| | | | - Scott A Rivkees
- Department of Pediatrics, Child Health Research Institute, College of Medicine, University of Florida, Gainesville, FL, USA
| | - Christopher C Wendler
- Department of Pediatrics, Child Health Research Institute, College of Medicine, University of Florida, Gainesville, FL, USA
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5
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Wu SJ, Furlan SN, Mihalas AB, Kaya-Okur HS, Feroze AH, Emerson SN, Zheng Y, Carson K, Cimino PJ, Keene CD, Sarthy JF, Gottardo R, Ahmad K, Henikoff S, Patel AP. Single-cell CUT&Tag analysis of chromatin modifications in differentiation and tumor progression. Nat Biotechnol 2021; 39:819-824. [PMID: 33846646 DOI: 10.1038/s41587-021-00865-z] [Citation(s) in RCA: 84] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Accepted: 02/18/2021] [Indexed: 12/12/2022]
Abstract
Methods for quantifying gene expression1 and chromatin accessibility2 in single cells are well established, but single-cell analysis of chromatin regions with specific histone modifications has been technically challenging. In this study, we adapted the CUT&Tag method3 to scalable nanowell and droplet-based single-cell platforms to profile chromatin landscapes in single cells (scCUT&Tag) from complex tissues and during the differentiation of human embryonic stem cells. We focused on profiling polycomb group (PcG) silenced regions marked by histone H3 Lys27 trimethylation (H3K27me3) in single cells as an orthogonal approach to chromatin accessibility for identifying cell states. We show that scCUT&Tag profiling of H3K27me3 distinguishes cell types in human blood and allows the generation of cell-type-specific PcG landscapes from heterogeneous tissues. Furthermore, we used scCUT&Tag to profile H3K27me3 in a patient with a brain tumor before and after treatment, identifying cell types in the tumor microenvironment and heterogeneity in PcG activity in the primary sample and after treatment.
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Affiliation(s)
- Steven J Wu
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.,Molecular Engineering & Sciences Institute, University of Washington, Seattle, WA, USA
| | - Scott N Furlan
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.,Department of Pediatrics, University of Washington, Seattle, WA, USA.,Brotman-Baty Institute for Precision Medicine, University of Washington, Seattle, WA, USA
| | - Anca B Mihalas
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.,Department of Neurological Surgery, University of Washington, Seattle, WA, USA
| | - Hatice S Kaya-Okur
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.,Howard Hughes Medical Institute, Seattle, WA, USA.,Altius Institute for Biomedical Sciences, Seattle, WA, USA
| | - Abdullah H Feroze
- Department of Neurological Surgery, University of Washington, Seattle, WA, USA
| | - Samuel N Emerson
- Department of Neurological Surgery, University of Washington, Seattle, WA, USA
| | - Ye Zheng
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Kalee Carson
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Patrick J Cimino
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.,Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - C Dirk Keene
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Jay F Sarthy
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.,Department of Pediatrics, University of Washington, Seattle, WA, USA
| | - Raphael Gottardo
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Kami Ahmad
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Steven Henikoff
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA. .,Howard Hughes Medical Institute, Seattle, WA, USA.
| | - Anoop P Patel
- Brotman-Baty Institute for Precision Medicine, University of Washington, Seattle, WA, USA. .,Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA. .,Department of Neurological Surgery, University of Washington, Seattle, WA, USA.
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6
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Zheng Y, Wang Z, Wei S, Liu Z, Chen G. Epigenetic silencing of chemokine CCL2 represses macrophage infiltration to potentiate tumor development in small cell lung cancer. Cancer Lett 2020; 499:148-163. [PMID: 33253790 DOI: 10.1016/j.canlet.2020.11.034] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2019] [Revised: 11/18/2020] [Accepted: 11/21/2020] [Indexed: 12/20/2022]
Abstract
Highly invasive and rapidly fatal, small-cell lung cancer (SCLC) has been an insurmountable gulf since discovery. Innate immunity plays a vital role in anti-tumor response, among which macrophages contribute to an indispensable character. Here, we found that macrophage infiltration in SCLC reduced significantly in a stage-dependent manner, attributed to the decreased expression of CCL2, a potent chemoattractant for monocytes. Validated by ChIP-qPCR and MassArray methylation analysis, CCL2 expression was inhibited by EZH2-mediated H3K27me3 in the enhancer regions and DNMT1-mediated DNA methylation in the promoter regions, the process of which could be reversed by small-molecular compounds, EPZ011989 and Decitabine. Direct cell-cell contact between SCLC cells and macrophages skewed the phenotype of macrophages to be more M1-like. Furthermore, in an ectopic engraft model of SCLC, disruption of EZH2/DNMT1 function using the combination treatment of EPZ011989 and Decitabine potently abrogated the inhibition of macrophage infiltration and thus suppressed tumor growth, the effect of which was impaired by CCL2 neutralization or macrophage depletion. Overall, this work provides new insights into the role of macrophages in SCLC and establishes a rationale for constructing novel therapeutic avenues for SCLC patients.
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Affiliation(s)
- Yang Zheng
- Department of Oncology, First Hospital, Jilin University, 130012, Jilin, PR China.
| | - Zhihong Wang
- Institute of Pharmacology and Toxicology, Academy of Military Medical Sciences, 100850, Beijing, PR China; School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing, 210009, PR China
| | - Simeng Wei
- Department of Oncology, First Hospital, Jilin University, 130012, Jilin, PR China
| | - Ziling Liu
- Department of Oncology, First Hospital, Jilin University, 130012, Jilin, PR China.
| | - Guojiang Chen
- Institute of Pharmacology and Toxicology, Academy of Military Medical Sciences, 100850, Beijing, PR China.
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7
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Zhao X, Tian GG, Fang Q, Pei X, Wang Z, Wu J. Comparison of RNA m 6A and DNA methylation profiles between mouse female germline stem cells and STO cells. MOLECULAR THERAPY. NUCLEIC ACIDS 2020; 23:431-439. [PMID: 33473328 PMCID: PMC7803632 DOI: 10.1016/j.omtn.2020.11.020] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Accepted: 11/17/2020] [Indexed: 11/17/2022]
Abstract
N6-methyladenosine (m6A) methylation modification is the most prevalent and abundant internal modification of eukaryotic mRNAs. Increasing evidence has shown that mRNA m6A plays important roles in the development of stem cells. However, to the best of our knowledge, no reports about the roles of mRNA m6A in mouse female germline stem cells (mFGSCs) have been published. In this study, we compared the genome-wide profiles of mRNA m6A methylation and DNA methylation between FGSCs and sandosinbred mice (SIM) embryo-derived thioguanine and ouabain-resistant (STO) cells. qRT-PCR revealed that the expression levels of mRNA m6A-related genes (Mettl3, Alkbh5, Ythdf1, Ythdf2, Ythdc1, and Ythdc2) in FGSCs were significantly higher than those in STO cells. m6A RNA immunoprecipitation sequencing (MeRIP-seq) data further showed that the unique m6A-methylated mRNAs in FGSCs and STO cells were related to cell population proliferation and somatic development, respectively. Additionally, knockdown of Ythdf1 inhibited FGSC self-renewal. Comparison of methylated DNA immunoprecipitation sequencing (MeDIP-seq) results between FGSCs and STO cells identified that DNA methylation contributed to FGSC proliferation by suppressing the somatic program. These results suggested that m6A regulated FGSC self-renewal possibly through m6A binding protein YTHDF1, and DNA methylation repressed somatic programs in FGSCs to maintain FGSC characteristics.
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Affiliation(s)
- Xinyan Zhao
- Key Laboratory of Fertility Preservation and Maintenance of Ministry of Education, Ningxia Medical University, Yinchuan 750004, China
| | - Geng G Tian
- Key Laboratory for the Genetics of Developmental & Neuropsychiatric Disorders (Ministry of Education), Bio-X Institutes, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Qian Fang
- Key Laboratory for the Genetics of Developmental & Neuropsychiatric Disorders (Ministry of Education), Bio-X Institutes, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Xiuying Pei
- Key Laboratory of Fertility Preservation and Maintenance of Ministry of Education, Ningxia Medical University, Yinchuan 750004, China
| | - Zhaoxia Wang
- Laboratory Animal Center, Instrumental Analysis Center, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Ji Wu
- Key Laboratory of Fertility Preservation and Maintenance of Ministry of Education, Ningxia Medical University, Yinchuan 750004, China.,Key Laboratory for the Genetics of Developmental & Neuropsychiatric Disorders (Ministry of Education), Bio-X Institutes, Shanghai Jiao Tong University, Shanghai 200240, China.,Shanghai Key Laboratory of Reproductive Medicine, Shanghai, China
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8
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Lapsley CR, Irwin R, McLafferty M, Thursby SJ, O'Neill SM, Bjourson AJ, Walsh CP, Murray EK. Methylome profiling of young adults with depression supports a link with immune response and psoriasis. Clin Epigenetics 2020; 12:85. [PMID: 32539844 PMCID: PMC7477873 DOI: 10.1186/s13148-020-00877-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Accepted: 05/28/2020] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Currently the leading cause of global disability, clinical depression is a heterogeneous condition characterised by low mood, anhedonia and cognitive impairments. Its growing incidence among young people, often co-occurring with self-harm, is of particular concern. We recently reported very high rates of depression among first year university students in Northern Ireland, with over 25% meeting the clinical criteria, based on DSM IV. However, the causes of depression in such groups remain unclear, and diagnosis is hampered by a lack of biological markers. The aim of this exploratory study was to examine DNA methylation patterns in saliva samples from individuals with a history of depression and matched healthy controls. RESULTS From our student subjects who showed evidence of a total lifetime major depressive event (MDE, n = 186) we identified a small but distinct subgroup (n = 30) with higher risk scores on the basis of co-occurrence of self-harm and attempted suicide. Factors conferring elevated risk included being female or non-heterosexual, and intrinsic factors such as emotional suppression and impulsiveness. Saliva samples were collected and a closely matched set of high-risk cases (n = 16) and healthy controls (n = 16) similar in age, gender and smoking status were compared. These showed substantial differences in DNA methylation marks across the genome, specifically in the late cornified envelope (LCE) gene cluster. Gene ontology analysis showed highly significant enrichment for immune response, and in particular genes associated with the inflammatory skin condition psoriasis, which we confirmed using a second bioinformatics approach. We then verified methylation gains at the LCE gene cluster at the epidermal differentiation complex and at MIR4520A/B in our cases in the laboratory, using pyrosequencing. Additionally, we found loss of methylation at the PSORSC13 locus on chromosome 6 by array and pyrosequencing, validating recent findings in brain tissue from people who had died by suicide. Finally, we could show that similar changes in immune gene methylation preceded the onset of depression in an independent cohort of adolescent females. CONCLUSIONS Our data suggests an immune component to the aetiology of depression in at least a small subgroup of cases, consistent with the accumulating evidence supporting a relationship between inflammation and depression. Additionally, DNA methylation changes at key loci, detected in saliva, may represent a valuable tool for identifying at-risk subjects.
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Affiliation(s)
- Coral R Lapsley
- Northern Ireland Centre for Stratified Medicine, School of Biomedical Sciences, Ulster University, C-TRIC, Altnagelvin Hospital, Derry/Londonderry, UK
| | - Rachelle Irwin
- Genomics Medicine Research Group, School of Biomedical Sciences, Ulster University, Coleraine Campus, Coleraine, UK
| | - Margaret McLafferty
- Northern Ireland Centre for Stratified Medicine, School of Biomedical Sciences, Ulster University, C-TRIC, Altnagelvin Hospital, Derry/Londonderry, UK.,School of Psychology, Ulster University, Coleraine Campus, Coleraine, UK
| | - Sara Jayne Thursby
- Genomics Medicine Research Group, School of Biomedical Sciences, Ulster University, Coleraine Campus, Coleraine, UK
| | - Siobhan M O'Neill
- School of Psychology, Ulster University, Coleraine Campus, Coleraine, UK
| | - Anthony J Bjourson
- Northern Ireland Centre for Stratified Medicine, School of Biomedical Sciences, Ulster University, C-TRIC, Altnagelvin Hospital, Derry/Londonderry, UK
| | - Colum P Walsh
- Genomics Medicine Research Group, School of Biomedical Sciences, Ulster University, Coleraine Campus, Coleraine, UK
| | - Elaine K Murray
- Northern Ireland Centre for Stratified Medicine, School of Biomedical Sciences, Ulster University, C-TRIC, Altnagelvin Hospital, Derry/Londonderry, UK.
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9
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Thursby SJ, Lobo DK, Pentieva K, Zhang SD, Irwin RE, Walsh CP. CandiMeth: Powerful yet simple visualization and quantification of DNA methylation at candidate genes. Gigascience 2020; 9:5860739. [PMID: 32568373 PMCID: PMC7307318 DOI: 10.1093/gigascience/giaa066] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Revised: 04/12/2020] [Accepted: 05/26/2020] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND DNA methylation microarrays are widely used in clinical epigenetics and are often processed using R packages such as ChAMP or RnBeads by trained bioinformaticians. However, looking at specific genes requires bespoke coding for which wet-lab biologists or clinicians are not trained. This leads to high demands on bioinformaticians, who may lack insight into the specific biological problem. To bridge this gap, we developed a tool for mapping and quantification of methylation differences at candidate genomic features of interest, without using coding. FINDINGS We generated the workflow "CandiMeth" (Candidate Methylation) in the web-based environment Galaxy. CandiMeth takes as input any table listing differences in methylation generated by either ChAMP or RnBeads and maps these to the human genome. A simple interface then allows the user to query the data using lists of gene names. CandiMeth generates (i) tracks in the popular UCSC Genome Browser with an intuitive visual indicator of where differences in methylation occur between samples or groups of samples and (ii) tables containing quantitative data on the candidate regions, allowing interpretation of significance. In addition to genes and promoters, CandiMeth can analyse methylation differences at long and short interspersed nuclear elements. Cross-comparison to other open-resource genomic data at UCSC facilitates interpretation of the biological significance of the data and the design of wet-lab assays to further explore methylation changes and their consequences for the candidate genes. CONCLUSIONS CandiMeth (RRID:SCR_017974; Biotools: CandiMeth) allows rapid, quantitative analysis of methylation at user-specified features without the need for coding and is freely available at https://github.com/sjthursby/CandiMeth.
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Affiliation(s)
- Sara-Jayne Thursby
- Genomic Medicine Research Group, School of Biomedical Sciences, Ulster University, 1 Cromore Road, Coleraine, BT52 1SA, UK
| | - Darin K Lobo
- Genomic Medicine Research Group, School of Biomedical Sciences, Ulster University, 1 Cromore Road, Coleraine, BT52 1SA, UK
- Present address: Republic Polytechnic, 9 Woodlands Avenue 9, Singapore 738964
| | - Kristina Pentieva
- Nutrition Innovation Centre for Food & Health (NICHE), School of Biomedical Sciences, Ulster University, 1 Cromore Road, Coleraine, BT52 1SA, UK
| | - Shu-Dong Zhang
- Stratified Medicine Research Groups, School of Biomedical Sciences, Ulster University, 1 Cromore Road, Coleraine, BT52 1SA, UK
| | - Rachelle E Irwin
- Stratified Medicine Research Groups, School of Biomedical Sciences, Ulster University, 1 Cromore Road, Coleraine, BT52 1SA, UK
| | - Colum P Walsh
- Correspondence address. Colum P. Walsh, Genomic Medicine Research Group, School of Biomedical Sciences, Ulster University UK. Tel: +44 28 7012 4484; E-mail:
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10
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Song L, Kim DS, Gou W, Wang J, Wang P, Wei Z, Liu B, Li Z, Gou K, Wang H. GRP94 regulates M1 macrophage polarization and insulin resistance. Am J Physiol Endocrinol Metab 2020; 318:E1004-E1013. [PMID: 32208002 PMCID: PMC7311672 DOI: 10.1152/ajpendo.00542.2019] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Revised: 02/24/2020] [Accepted: 03/12/2020] [Indexed: 11/22/2022]
Abstract
Macrophage polarization contributes to obesity-induced insulin resistance. Glucose-regulated protein 94 (GRP94) is an endoplasmic reticulum (ER) chaperone specialized for folding and quality control of secreted and membrane proteins. To determine the role of GRP94 in macrophage polarization and insulin resistance, macrophage-specific GRP94 conditional knockout (KO) mice were challenged with a high-fat diet (HFD). Glucose tolerance, insulin sensitivity, and macrophage composition were compared with control mice. KO mice showed better glucose tolerance and increased insulin sensitivity. Adipose tissues from HFD-KO mice contained lower numbers of M1 macrophages, with lower expression of M1 macrophage markers, than wild-type (WT) mice. In vitro, WT adipocytes cocultured with KO macrophages retained insulin sensitivity, whereas those cultured with WT macrophages did not. In addition, compared with WT bone marrow-derived macrophages (BMDMs), BMDMs from GRP94 KO mice exhibited lower expression of M1 macrophage marker genes following stimulation with LPS or IFN-γ, and exhibited partially increased expression of M2 macrophage marker genes following stimulation with interleukin-4. These findings identify GRP94 as a novel regulator of M1 macrophage polarization and insulin resistance and inflammation.
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Affiliation(s)
- Lili Song
- State Key Laboratory of Agrobiotechnology, College of Biological Science, China Agricultural University, Beijing, China
- Department of Surgery, Medical University of South Carolina, Charleston, South Carolina
| | - Do-Sung Kim
- Department of Surgery, Medical University of South Carolina, Charleston, South Carolina
| | - Wenyu Gou
- Department of Surgery, Medical University of South Carolina, Charleston, South Carolina
| | - Jingjing Wang
- Department of Surgery, Medical University of South Carolina, Charleston, South Carolina
| | - Ping Wang
- Department of Surgery, Medical University of South Carolina, Charleston, South Carolina
| | - Zhiguo Wei
- Department of Surgery, Medical University of South Carolina, Charleston, South Carolina
| | - Bei Liu
- Department of Medicine, Medical University of South Carolina, Charleston, South Carolina
| | - Zihai Li
- Department of Medicine, Medical University of South Carolina, Charleston, South Carolina
| | - Kemian Gou
- Institute of Comparative Medicine, College of Veterinary Medicine, Yangzhou University, Yangzhou, China
| | - Hongjun Wang
- Department of Surgery, Medical University of South Carolina, Charleston, South Carolina
- Ralph H. Johnson Veterans Affairs Medical Center, Charleston, South Carolina
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11
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Interleukin 1β and Prostaglandin E2 affect expression of DNA methylating and demethylating enzymes in human gingival fibroblasts. Int Immunopharmacol 2019; 78:105920. [PMID: 31810887 DOI: 10.1016/j.intimp.2019.105920] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Revised: 08/28/2019] [Accepted: 09/15/2019] [Indexed: 02/06/2023]
Abstract
Periodontitis is a common chronic inflammatory condition that results in increased levels of inflammatory cytokines and inflammatory mediators. In addition to oral disease and tooth loss, it also causes low-grade systemic inflammation that contributes to development of systemic conditions including cardiovascular disease, pre-term birth, diabetes and cancer. Chronic inflammation is associated with epigenetic change, and it has been suggested that such changes can alter cell phenotypes in ways that contribute to both ongoing inflammation and development of associated pathologies. Here we show that exposure of human gingival fibroblasts to IL-1β increases expression of maintenance methyltransferase DNMT1 but decreases expression of de novo methyltransferase DNMT3a and the demethylating enzyme TET1, while exposure to PGE2 decreases expression of all three enzymes. IL-1β and PGE2 both affect global levels of DNA methylation and hydroxymethylation, as well as methylation of some specific CpG in inflammation-associated genes. The effects of IL-1β are independent of its ability to induce production of PGE2, and the effects of PGE2 on DNMT3a expression are mediated by the EP4 receptor. The finding that exposure of fibroblasts to IL-1β and PGE2 can result in altered expression of DNA methylating/demethylating enzymes and in changing patterns of DNA methylation suggests a mechanism through which inflammatory mediators might contribute to the increased risk of carcinogenesis associated with inflammation.
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12
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The diverse roles of DNA methylation in mammalian development and disease. Nat Rev Mol Cell Biol 2019; 20:590-607. [PMID: 31399642 DOI: 10.1038/s41580-019-0159-6] [Citation(s) in RCA: 1064] [Impact Index Per Article: 212.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/08/2019] [Indexed: 12/22/2022]
Abstract
DNA methylation is of paramount importance for mammalian embryonic development. DNA methylation has numerous functions: it is implicated in the repression of transposons and genes, but is also associated with actively transcribed gene bodies and, in some cases, with gene activation per se. In recent years, sensitive technologies have been developed that allow the interrogation of DNA methylation patterns from a small number of cells. The use of these technologies has greatly improved our knowledge of DNA methylation dynamics and heterogeneity in embryos and in specific tissues. Combined with genetic analyses, it is increasingly apparent that regulation of DNA methylation erasure and (re-)establishment varies considerably between different developmental stages. In this Review, we discuss the mechanisms and functions of DNA methylation and demethylation in both mice and humans at CpG-rich promoters, gene bodies and transposable elements. We highlight the dynamic erasure and re-establishment of DNA methylation in embryonic, germline and somatic cell development. Finally, we provide insights into DNA methylation gained from studying genetic diseases.
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13
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Mackin SJ, Thakur A, Walsh CP. Imprint stability and plasticity during development. Reproduction 2018; 156:R43-R55. [PMID: 29743259 DOI: 10.1530/rep-18-0051] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Accepted: 05/08/2018] [Indexed: 12/20/2022]
Abstract
There have been a number of recent insights in the area of genomic imprinting, the phenomenon whereby one of two autosomal alleles is selected for expression based on the parent of origin. This is due in part to a proliferation of new techniques for interrogating the genome that are leading researchers working on organisms other than mouse and human, where imprinting has been most studied, to become interested in looking for potential imprinting effects. Here, we recap what is known about the importance of imprints for growth and body size, as well as the main types of locus control. Interestingly, work from a number of labs has now shown that maintenance of the imprint post implantation appears to be a more crucial step than previously appreciated. We ask whether imprints can be reprogrammed somatically, how many loci there are and how conserved imprinted regions are in other species. Finally, we survey some of the methods available for examining DNA methylation genome-wide and look to the future of this burgeoning field.
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Affiliation(s)
- Sarah-Jayne Mackin
- Genomic Medicine Research GroupSchool of Biomedical Sciences, Ulster University, Northern Ireland, UK
| | - Avinash Thakur
- Genomic Medicine Research GroupSchool of Biomedical Sciences, Ulster University, Northern Ireland, UK
| | - Colum P Walsh
- Genomic Medicine Research GroupSchool of Biomedical Sciences, Ulster University, Northern Ireland, UK
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